Comprehensive analysis of long noncoding RNAs and lncRNA-mRNA networks in snakehead (Channa argus) response to Nocardia seriolae infection

Fish Shellfish Immunol. 2023 Jan 20;108558. doi: 10.1016/j.fsi.2023.108558. Online ahead of print.

Abstract

Evidence has been demonstrated that lncRNAs were involved in a variety of immune responses in vertebrate. It has been demonstrated that immune-related lncRNAs play functions in immune regulation against pathogenic bacterial infections in teleost. Nocardia seriolae, as one of the Gram-positive bacteria, can cause chronic systemic granulomatous disease for snakehead (Channa argus). However, how lncRNAs function in the immune regulation process once snakehead was infected with N. seriolae infection has not been studied so far. Accordingly, transcription landscapes of lncRNAs and mRNAs in snakehead were investigated. A total of 1991 lncRNA were obtained. Co-localization and co-expression analyses predicted 57,584 co-expression and 16,047 co-location lncRNA-mRNA pairs. To further analyze the potential function of lncRNAs in these pairs, GO enrichment analysis and KEGG signal pathway were performed on the target mRNAs of the differently expressed lncRNAs, which suggested that lncRNAs may play essential roles in modulating mRNA expression levels and subsequently trigger downstream immune signaling pathways to regulate the immune response to pathogen infections in fish. In addition, 9 DEmRNA and 3 lncRNAs were randomly selected for qRT-PCR analyzed, which confirmed the accuracy of transcriptome data analysis. These results can provide novel knowledge about lncRNAs in immune responses process in snakehead, and could serve as important resources for further investigating the roles of lncRNAs during pathogen infections in teleost.

Keywords: Channa argus; Intestine; Long non-coding RNA; Nocardia seriolae; mRNA.